[gmx-users] after genbox

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Dec 5 09:48:08 CET 2012

Hi Nur,

80:20 is equal to four liters to one. One liter of water is 55.4 mole. If
you know how many moles of the other goes into four liters, divide the
number by 55.4 and you know how many you need to add per water molecule.
Then multiply by the number of water molecules to know the number of
molecules to ADD. If you're going to replace, you have to make a
correction. But it's pretty straightforward math.



On Wed, Dec 5, 2012 at 4:20 AM, Nur Syafiqah Abdul Ghani
<pqah123 at gmail.com>wrote:

> Hi guys,
> I'm doing simulation with mix-solvent which is hexafluoroisopropaonol
> and water and it needs percentage v/v.The percentage for the ration is
> 80% of hfip and 20% water..
> I already put the solvent by using using the command
> genbox -cp protein_box.gro -ci hfi.gro -nmol 1000 -cs spc216.gro -p
> control.top -o protein_mix.gro
> So,i already got the value and my question is,how i want to calculate
> the percentage of the ratio to make sure the % is the one that i want?
> --
> Best Regards,
> Nur Syafiqah Abdul Ghani,
> Theoretical and Computational Chemistry Laboratory,
> Department of Chemistry,
> Faculty of Science,
> Universiti Putra Malaysia,
> 43400 Serdang,
> Selangor.
> 013-7188131
> alternative email : syafiqahabdulghani at gmail.com
> --
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4

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